I've used vanilla jk3 SDK, so you'll first have to get it to compile. Go download and install MS Visual C++ 2008 Express edition, if you haven't already. Then download and apply these code fixes. Open the solution in Visual Studio (double-click on codemp\JKA_mp(SDK).sln in Windows Explorer), then try and build the whole solution. If three DLLs have been produced in codemp\Debug, you're ready to go.

Now to the actual mod:
You'll have to edit codemp\game\w_force.c (the mod is serverside; if that won't do, tell me and I'll look into it again).
So in Visual Studio, in the left hand tree view, double-click on JK2game/Source Files/w_force.c.

First, you'll have to define which force powers are supposed to switch the saber off. On top of w_force.c, right after the #include's, add the following piece of

and then remove the comment signs (//) in front of the chosen force powers.

Now we're going to switch the saber off in WP_ForcePowerStart(...).
Jump to that function (on top of the right hand edit view, there are two list boxes right under the filename thingy; the left one should read "(Global Scope)", the right one should be empty; open the right one and select said function from the list).
You'll find a lengthy "switch" construct in the function (there's only one, so that shouldn't be a problem). Right after the switch block, insert the section indicated in this

(BTW, this is mostly copied from the taunt command; following your idea, I just looked it up there, copied it and it worked like a charm; then I've modified it a bit to accomodate for the automatic re-ignition later).
Well, that's it for the deactivation part.

Finally, to re-activate the saber after all saber-deactivating powers are done, you'll have to edit - guess what - right, WP_ForcePowerStop(...). So jump there, and at the end of the function, add the section indicated in the following snippet of

That's it. Now you'll just have to re-build the server (in the left hand tree view, right-click on "JK2game" and select "Build"), then pack the produced jampgamex86.dll up in a pk3 (you only need jampgamex86.dll since it's a serverside only mod) and put it in your base folder.

I've tried this mod with most force powers, and here's the deal:
- It doesn't seem to work at all for "heal" and "jump" (looks like WP_ForcePowerStart isn't called for these)
- For "push" and "pull" the deactivation part works, but the re-activation doesn't (WP_ForcePowerStop isn't called for these; they're kinda instant powers).
If you do want the de/re-activation for any of those force powers as well, say so and I'll look into again (otherwise I'd rather not).

What I haven't tried at all is "team heal" and "team energize". Also, I haven't tested the mod with dual sabers / staff. I'll leave that all to you.

And one more shortcoming (sort of): If you define any of the long-term force powers (see, speed, protect, absorb) as saber-deactivating, there's nothing that hinders you to activate the saber again while the force power's still active. If this is a problem, say so and I'll try to find a way around that (though that's likely more difficult to accomplish).